Intracellular protein breakdown carries out essential cellular functions, such as the modulation of levels of regulatory proteins and the removal of abnormal or damaged proteins. The long-term objective of this research is the elucidation of the biochemical mechanisms of protein breakdown. Our previous studies showed that ubiquitin, a 76-amino acid polypeptide, is involved in selective protein breakdown. In this pathway, proteins destined for degradation are first ligated to ubiquitin, and then are degraded by enzymes that specifically recognize ubiquitin-conjugated proteins. We have described several enzymatic reactions in the formation and breakdown of ubiquitin- protein conjugates and characterized binding sites of ubiquitin ligase that allow the recognition of some protein structures suitable for degradation. However, we still know very little about the mode of action and specificity of the ligase, a key enzyme in the commitment of proteins for degradation. Another "black box" is the ATP-dependent enzyme system that degrades proteins conjugated to ubiquitin, the mode of action of which is completely obscure. We now wish to gain insight into these important problems. We shall investigate the existence of multiple species of ligase, each specific for a certain type of protein substrate. Possible recognition sequences in proteins will be tested by the action of synthetic peptides on ligase- protein interaction. The special role of the a-NH2 group of proteins will be investigated by the characterization of ubiquitin ligation to and removal from the a-NH2 group. Three factors involving the degradation of ubiquitin-conjugated proteins will be purified and used to define the role of ATP and the intermediary reactions in this process. Because of its important cellular roles, the delineation of the mode of action of the ubiquitin pathway is of basic importance and may help in the future understanding of disorders of protein metabolism.